Introduction

Biology is defined as the study of life / living things. A living thing is defined as anything that converts energy from one form to another, while using that energy to grow, change, and reproduce.

NOTE: Primary source for these notes is Khan Academy's HS Biology course, with additional information from Wikipedia and other sources.

Scientific Method

The scientific method is the standard guideline for discovery and experimentation in the sciences (chemistry, physics, biology, etc..) The basic steps are...

  1. Observe.
  2. Ask a question about the observation.
  3. Make a guess that answers the question (hypothesis).
  4. Test the guess to see if it's correct (experiment).
  5. Refine and iterate.

The last step (refine and iterate) just means that you do it all over again but make changes based on the things you learned from your experiment. For example, ...

Hypothesis

The scientific method revolves around making an observation and coming up with a testable explanation for that observation -- called a hypothesis. If the explanation isn't testable, you can't consider it a hypothesis. For example, a good hypothesis may be that increased sun exposure leads to an increased risk of skin cancer because it's something you can test. A bad explanation may be that exposure to centaurs increase the risk of skin cancer because centaurs don't exist (and as such the hypothesis can't be tested).

NOTE: The material mentions that for a hypothesis to be testable, you should be able to come up with an experiment that shows that its false -- it's falsifiable. How you word your hypothesis is typically what determines if it's testable/falsifiable -- when you read the hypothesis, what defines a failure?
NOTE: A hypothesis and a theory are different things. Hypothesis is a potential answer for a specific problem. A theory provides a potential framework for a much broader class of problems based on supporting evidence. The example given by the material: "The toaster won't toast because the electrical outlet is broken" is a hypothesis, whereas "Electrical appliances need a source of electricity in order to run" is closer to a theory.

Experiment

Once you have a hypothesis, you design an experiment to test it. In the case of our sun exposure leads to increased risk of skin cancer hypothesis, an experiment may be to expose skin cells to UV rays in amounts equivalent to that given off by the sun and then check to see if those cells have been damaged (compared to a control group of skin cells that you haven't exposed to UV rays).

What makes a good experiment?

NOTE: There's always at least one control group in any experiment to provide a baseline. There's no limit to the number of experimental groups -- each group may have a slightly different type/amount of treatment applied.
NOTE: Because things are so wishy-washy/not-exactly in biology, it's typical for an experiments to be repeated multiple times and to have a large sample size -- the larger our sample sizes and the more times we conduct the experiment, the more we can be confident of our result. What do I mean by wishy-washy? Genetic variation between samples may result in different types/levels of responses. For example, people with a certain gene may respond quicker to certain drugs than people who don't produce that gene.

Other terminology around the scientific method...

NOTE: You can have more than one independent variable if you follow specific guidelines and are experienced enough, but the general rule of thumb is to have only 1 independent variable just because it makes things much simpler to analyze/interpret.

Chemistry

An element is matter that cannot be broken down any further by chemical reaction -- it's a substance made entirely out of one type of atom. Each element/atom has a specific set of properties that defines how it acts/reacts (e.g. weight, colour, how light reflects, etc..).

Examples of elements/atoms:

Examples of non-elements:

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The building blocks of atoms are protons, neutrons, and electrons. Protons and neutrons form the nucleus of the atom while electrons jump around outside of the nucleus. Protons and electrons are attracted to each other -- protons are positively charged while electrons are negatively charged. Although, protons and electrons never fully meet (electrons are always buzzing/hovering around the outside of the nucleus where the protons are).

The configuration of an atom (protons/neutrons/electrons) is what allows us to predicate how one element may react to another element. For example, certain elements may attract, repel, bond, swipe electrons, etc..

The number of protons are what defines the type of atom/element. For example, hydrogen has 1 proton, helium as 2, lithium has 3, etc.. The number of neutrons and electrons can change without changing the type of element as long as the number of protons remain the same.

The periodic table below orders elements/atoms by the number of protons (also called the atomic number)...

By Offnfopt - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=62296883

NOTE: A different number of neutrons = different version of the same element. For example, Carbon-12 (6 neutrons) and Carbon-13 (7 neutrons).

When atoms bind together, they form a molecule. Each type of molecule has the same configuration of atoms -- same atoms in the same numbers, structured/shaped similarly. For example, a water molecule is made up of 2 hydrogen atoms and 1 oxygen atom binding together in a house-roof shape...

By Dan Craggs - Own workThis vector image includes elements that have been taken or adapted from this:  Water-2D-labelled.png., Public Domain, https://commons.wikimedia.org/w/index.php?curid=7916072

NOTE: As far as I can tell, the atoms will always bind in the same way. You can't ever have a molecule that has the same types of atoms in the same numbers but with a different structure.

A monomer is a special designation for atoms/molecules that are able to join with other monomers to create even larger molecules. The process of joining is called polymerization and the resulting molecule is called a polymer.

Graphviz Dot Diagram

If the monomers that make up a polymer are all the same, the polymer is called a homopolymer. Otherwise, it's called a heteropolymer / copolymer.

For example, the glucose molecule is a monomer. It can combine with other glucose molecules to create the glycogen molecule, which is a polymer / homopolymer. Other examples of polymers (according to Wikipedia): amino acids and nucleotides (DNA).

NOTE: There are probably special properties to monomers that allow them to chain up. The Wikipedia page talks about a feature of monomers being a "carbon double bond" which is what allows them to form polymers.

Polymers are often referred to as macromolecules -- molecules that have a very large number of atoms.

An ion is a charged atom or molecule. A charged atom/molecule just means that it has an unequal number of protons and electrons:

Ions are always trying to lose their charge and become neutral, either by giving up an electrons or pulling in an electrons such that the the number of protons and electrons become equal. As such, ions will attract towards oppositely charged ions and repel from similarly charged ions:

pH

pH stands for potential of hydrogen and it's the measure of positively charged hydrogen ions in a solution. The more...

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pH is scaled logarithmically from 1 to 14. Each notch on the scale moves the acidity/basicity by a factory of 10. Going...

For example, going from 7 to 4 increases acidity by 1000x times / decreases basicity by 1000x.

The closer to...

NOTE: https://www.quora.com/Why-is-pure-water-considered-neutral -- Since pH is defined as the negative log of the hydrogen ion concentration, the pH of pure water is 7 or neutral. Pure water is neutral because the number of positive hydrogen ions produced is equal to the number of negative.

Carbohydrate Molecules

Carbohydrates (also called saccharides) are molecules that consist of a mix of carbon, hydrogen, and oxygen atoms. In biological systems, carbohydrates are often associated with...

NOTE: It was never explained what 'structural role' actually means.

The term monosaccharide is just means a carbohydrate that's a monomer (e.g. glucose). Similarly, the term polysaccharide means a carbohydrate built from other monosaccharides (e.g. glycogen is made of chained glucose).

Graphviz Dot Diagram

Protein Molecules

Proteins are molecules that consist of monomers called amino acids. The amino acids get chained together into a polymer called a polypeptide chain, and one or more polypeptide chains fold to a 3D structure and combine to become a protein. The 3D structure / shape of the protein (how its folded) is what gives it its abilities.

In biological systems, proteins are often associated with that facilitating some biological function. For example, the protein protease is responsible for breaking down food.

Graphviz Dot Diagram

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NOTE: The ribosome is what's responsible for folding? Not able to get a clear answer on this.

The basic structure of an amino acid is as follows. The R is a placeholder that, when set, defines what type of amino acid it is...

By GYassineMrabetTalk✉This W3C-unspecified vector image was created with Inkscape. - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=2551977

Lipid Molecules

Lipids are molecules that are somewhat not water soluble -- meaning that they have parts that resist water but maybe also parts that are attracted to water. In biological systems, lipids are often associated with...

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NOTE: Lipids are not always fats. All fats are lipids but not all lipids are fats.

Water Molecule

Water is essential to life -- it has unique properties that almost all biological processes depend on.

Recall that...

  1. a water molecule consists of 2 hydrogen atoms connected to an oxygen atom via covalent bonds. A covalent bond is a pair of electrons that both atoms share, thus bonding the atoms together.
  2. the position of an electron is based on probability. Electrons aren't fixed in a certain position or neatly orbiting around a nucleus as certain diagrams show. Rather, they're constantly buzzing/hopping around the nucleus. Depending on their environment, they may be more likely to be at certain locations vs other locations.

Oxygen atoms are extremely electronegative, meaning that oxygen has the propensity to pull the buzzing/hopping electrons more around itself than the atoms it's bound to. As such, in a water molecule, the electrons will spend more time solely around the oxygen atom than they do the hydrogen atom or a position that binds the hydrogen and oxygen together. This is what gives the oxygen atom in a water molecule a weakly negative charge (as indicated by δ-) while the hydrogen atoms have a weakly positive charge (as indicated by δ+). These types of charged molecules are called polar molecules.

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NOTE: Notice the shape of the water molecule in the diagram(s) above. Electron pairs are repelled from each other. They're also responsible for binding. That's what gives molecules their shapes/structure.

This weakly negative / weakly positive charge is what gives water several of the unique properties that biological properties depend on. Water molecules have a tendency to gravitate towards each other because the weakly negative oxygen atoms and the weakly positive hydrogen atoms of different water molecules attract. This attraction is called a hydrogen bond. Hydrogen bonds are weaker than covalent bonds in that the bonds aren't really solid -- water molecules can easily break off and go past each other.

By User Qwerter at Czech wikipedia: Qwerter. Transferred from cs.wikipedia to Commons by sevela.p. Translated to english by by Michal Maňas (User:snek01). Vectorized by Magasjukur2 - File:3D model hydrogen bonds in water.jpg, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=14929959

NOTE: The above paragraph is just giving the mechanics for how/why water is a liquid. Water is the only molecule that's liquid at room temperature? This can't be right -- see https://chemistry.stackexchange.com/q/76346. Why can't biological processes work in one of these other molecules just as they do in water? Maybe because they stay liquid at a shorter temperature range (e.g. 15-25C instead of 1-99C?

The weak attraction between water molecules is also what makes water a solvent. So long as they're polar molecules, other molecules can travel inside of water using the same attraction from weakly negative / weakly positive charges -- they gravitate and float around water molecules just as other water molecules do. For example, the cytoplasm of a cell is a solvent (mostly water). It works because other molecules in the cytoplasm (e.g. cellular machinery) can float around / travel around using the weakly negative / weakly positive charges.

Water is called a universal solvent because it can dissolve more molecules than other other liquid. Note that the term universal doesn't mean that it can dissolve everything, just that it can dissolve more things than the others.

The properties that make water conducive for biological processes to operate:

Other terminology related to water:

Cells

Cells are the basic unit of living things / the building blocks of life. They're tiny structures that encapsulate information and machinery that allows them to replicate/reproduce and perform other important functions (e.g. appendages to move around).

NOTE: Viruses are not cells but they may also be considered living because they reproduce in a roundabout way: the require machinery in the host cell to reproduce.

There are 2 types of cells: eukaryotic and prokaryotic. There main differences between them are that...

  1. the guts of eukaryotes are organized into organelles (membrane-bound compartments) where each one is responsible for some functionality, while prokaryotes have no organelles at all (guts are free floating).
  2. the DNA in eukaryotes into multiple independent segments (chromosomes), while prokaryotes have a single circular chain.

Other differences between eukaryotes and prokaryotes ...

Eukaryotes Prokaryotes
Size 10 to 100 micrometers (μm) 0.1 to 5 micrometers (μm)
Complexity More complex More simple
Sub-compartments (organelles) Yes No
DNA layout Multiple stands Single circular strand
Single-cell organisms Yes (e.g. amoeba) Yes (e.g. bacteria and archaea)
Multi-cell organisms Yes (e.g. animals and fungus) No
NOTE: Archaea is an organism that looks like bacteria but they're totally different.

Features

Different cell species vary in features. The subsections below detail common cell features (not exhaustive).

Some features are only present in certain cell speicies (e.g. only some cells have a flagellum tail) while other features are present in all cells but in different amounts (e.g. every cell has cytosol but larger cells have more cytosol).

Cytoplasm

The cytoplasm (both eukaryotic and prokaryotic) is the insides/guts of a cell. Cytosol refers to just the fluid, while cytoplasm refers to fluid as well as everything else inside the cell.

Every cell has cytoplasm.

Eukaryote with cell ribosomes highlighted

Membrane

The plasma membrane (present in both eukaryotic and prokaryotic cells) is the thing encapsulating the cytoplasm. It's what keeps the guys of the cell inside and controls the movement of substances coming into / going out of the cytoplasm.

Every cell has a membrane encapsulating its cytoplasm. Membranes in general follow the fluid mosaic model.

The term membrane can refer to either the plasma membrane or the membrane of a eukaryotic cell's organelle. How you should interpret it depends on the context in which its used.

Eukaryote with cell ribosomes highlighted

Prokaryotic with capsule highlighted

Facts about cell membranes:

Cell Wall

The cell wall (present in both eukaryotic and prokaryotic cells) is a stiff layer around the membrane meant for protection. Not all cells have a cell wall -- for example, animal cells don't but plant cells do. Technically, the cell wall (if it exists) isn't considered to be part of the cell. The membrane and everything in it is.

The material states that cell walls...

  1. provide an extra layer of protection.
  2. help maintain shape.
  3. help prevent dehydration.

Almost all prokaryotes have cell walls. Only some eukaryotes have cell walls (e.g. fungi and plants). The material says that cell walls for most bacteria are made up of a molecule called peptidoglycan, but it can be different for other cells. For example, this link says that plant cells have cell walls made up of cellulose.

Prokaryotic with capsule highlighted

Capsule

The Capsule (present in prokaryotic cell only) is the outermost layer of some types of cells (typically bacteria cells). Capsules are made up of carbohydrates and there mainly to help the cell stick itself to the environment.

Prokaryotic with capsule highlighted

NOTE: Although eukaryotic cells don't have capsules, they do have carbohydrates on their outside. Those carbohydrates aren't organized as a capsule though: https://www.quora.com/Do-some-eukaryotic-cells-have-capsules-or-is-it-just-prokaryotes-Are-there-exceptions-of-eukaryotes-having-capsules. Is this talking about the same carbohydrates that are embedded in the membrane (glycolipids / glycoproteins).

Ribosome

Ribosome (present in both eukaryotic and prokaryotic cells) are tiny molecular machines inside the cytoplasm that take in mRNA molecules (portions of DNA that have been written out) and produce proteins. Ribosomes themselves are structures made of proteins and RNA.

Ribosomes can either be floating around in the cytoplasm (called free ribosome) or be embedded in the membrane of endoplasmic reticulum.

Eukaryote with cell ribosomes highlighted

Appendage

Some cells have appendages that help them move (or stay put). There are different types of appendages...

Eukaryote with cell flagellum highlighted

Eukaryotic Cells

ANIMAL CELL

Eukaryotic plant cell

Eukaryotic cells are typically larger and have membrane-bound sub-compartments, called organelles, that hold in the guts of different regions of the cell. For example, their DNA is encapsulated in a organelle called the nucleus.

Eukaryotes have their DNA broken up into multiple strands. They can either be single-cellular organisms (e.g. amoeba) or multi-cellular organisms (e.g. human). Single-cellular organism that are eukaryotic are called protists.

The following are descriptions for some of the organelles shown in the diagram above.

Nucleus

Nucleus is an organelle that contains DNA (genetic information required for the functioning and replication). Both prokaryotic and eukaryotic cells have DNA, but only eukaryotic cells have a nucleus. In prokaryotic cells, the DNA flows around freely instead of being encapsulated in a nucleus.

 comprehensive diagram of a human cell nucleus.

Most eukaryotic cells contain a single nucleus, but some contain can have 0 and others can have more than one. An example of 0 is blood cells -- mature blood cells don't have any DNA, therefore no nucleus. An example of more than 1 is the organism Oxytricha trifillax -- it contains 2 nuclei, each containing different DNA (its DNA is fragmented across 2 nuclei).

Endoplasmic Reticulum

Endoplasmic Reticulum is layered membrane (organelle?) that surrounds the nucleus and is directly connected to pores on the nucleus. Large portions of the endoplasmic reticulum's membrane have ribosomes attached. The parts that have ribosomes attached are called rough endoplasmic reticulum while the parts that don't are called smooth endoplasmic reticulum.

NOTE: It's called rough endoplasmic reticulum because the ribosomes make the surface look rough.

a) The ER is a winding network of thin membranous sacs found in close association with the cell nucleus. The smooth and rough endoplasmic reticula are very different in appearance and function (source: mouse tissue). (b) Rough ER is studded with numerous ribosomes, which are sites of protein synthesis (source: mouse tissue). EM × 110,000. (c) Smooth ER synthesizes phospholipids, steroid hormones, regulates the concentration of cellular Ca++, metabolizes some carbohydrates, and breaks down certain toxins (source: mouse tissue). EM × 110,510. (Micrographs provided by the Regents of University of Michigan Medical School © 2012)

Recall that ribosomes are what translate mRNA to proteins. Since the endoplasmic reticulum is directly connected to the nucleus (via pores on the nucleus), it provides a fairly straight-forward path for protein generation: mRNA produced in the nucleus...

  1. travels to the endoplasmic reticulum via the connected pores,
  2. then travels to the membrane of the endoplasmic reticulum where it ends up hitting ribosomes embedded in the (thereby producing proteins).

Golgi

Golgi are layered membrane (organelle?) that look similar to rough endoplasmic reticulum but aren't attached to the nucleus. Golgi package molecules (e.g. proteins) for travel to either another part of the cell or outside of the cell. They do this by pinching off parts of their membrane to wrap around the molecule.

They're also responsible for building lysosomes (cell digestion machines).

NOTE: The terms golgi, golgi apparatus, golgi complex, and golgi body all refer to the same thing.

Golgi apparatus

Mitochondria

Mitochondria are organelles responsible for cellular respiration: the process of producing Adenosine Triphosphate (ATP) from molecules such as sugars. ATP is a chemical that provides energy to drive various biological processes (e.g. muscle contractions). As such, mitochondria are often referred to as "the power house of the cell."

Mitochondria

NOTE: Mitochondria exist in both animal and plant cells.

The major parts of chloroplast are...

Mitochondria have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis).

Unlike how normal offspring DNA gets produced by mixing DNA from both parents, mitochondrial DNA comes entirely from the mother's side.

Lysosome

Lysosomes are organelles (animal cells only) that help break down waste products / foreign substances by containing various enzymes and maintaining an acidic pH. Lysosomes are more often found in animals cells than plant and algae cells.

NOTE: According to the material, the evidence that they've been found in plant cells is recent.

Structure of Lysosome

Peroxisome

Peroxisomes are organelles that are similar to Lysosomes -- both are small organelles that break down unwanted substances. The difference is that peroxisomes have different types of enzymes that require oxygen (oxidative enzymes).

NOTE: The material says that peroxisomes make hydrogen peroxide: Similarly, structures called peroxisomes carry out chemical reactions called oxidation reactions and produce hydrogen peroxide, both of which would damage the cell if they weren’t safely stored away in their own “room.”

Basic structure of a peroxisome, showing the crystallized enzyme core as found in rat liver cells.

Chloroplast

Chloroplasts are organelle (only plant and algae cells) responsible for photosynthesis. Photosynthesis is the process of taking in light and using it to build sugars from water and carbon dioxide. Those sugars are then used by the mitochondria to produce energy in a process called cellular respiration.

Ultrastructure of a chloroplast.

The major parts of chloroplast are...

Chlorophyll is a pigment / compound found in chloroplast that absorbs light and uses it to produce carbohydrates. It's found in the thylakoid membrane as well as the stroma, and it only absorbs red and blue light (while reflecting green).

Like mitochondria, chloroplast have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis). A descendant of that organism may be cyanobacterium, which has a similar ability to generate sugars from light (see Wikipedia).

Vacuole

Vacuoles are organelle (mostly plant and algae cells) responsible for storage (water, food, waste?) and enzymes that help break things down. Vacuoles are typically found in plant and algae cells, but may also exist in animal cells. The ones in plants / algae tend to be much larger.

Vacuoles are often responsible for a plant's shape. For example, a well watered plant will be upright and spry because its vacuoles are full. A plant that isn't as well watered may be sagging down or wilting because the vacuoles are less full

By LadyofHats - did it myself based on [1], [2] ,[3] and [4]., Public Domain, https://commons.wikimedia.org/w/index.php?curid=1685428

Prokaryotic Cells

Prokaryotic cell

Prokaryotic cells: These cells are typically smaller and don't have organelles. For example, their DNA is free-floating in the cell (it's free floating but stays mostly in the center area called the nucleoid).

Prokaryotes have a single circular-strand of DNA. They can only be single-cellular organisms (e.g. bacteria).

Fluid Mosaic Model

The fluid mosaic model is the accepted model for how cell membranes work. The model says that a cell membrane is composed of a phospholipid bilayer with proteins, lipids, and carbohydrates floating around on either side or embedded in between.

NOTE: The description above is the rational for the name 'fluid mosaic model'. It's fluid and there's a mosaic of different things embedded or attached to it.

By LadyofHats Mariana Ruiz - Own work. Image renamed from File:Cell membrane detailed diagram.svg, Public Domain, https://commons.wikimedia.org/w/index.php?curid=6027169

A phospholipid is a amphipathic lipid molecule that involves a phosphate group. The...

NOTE: For a refresher on how hydrophobic / hydrophilic molecules work, see the section on Water. Specifically: adhesion / weakly negative / weakly positive.

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As such, phospholipids have a natural tendency to form as a phospholipid bilayer (2 layers attached together, called a liposome) or a ball (called a micelle). The hydrophilic heads are going to point towards the water causing the hydrophobic tails to point at each other.

By Mariana Ruiz Villarreal ,LadyofHats - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=3032610

NOTE: If the phospholipids have small tails, they may form a micelle (a small, single-layered sphere), while if they have bulkier tails, they may form a liposome.

How fluid a phospholipid bilayer is depends on the types of phospholipid molecules that make it up and the temperature. Phospholipid molecules have 2 fatty acid tails. The fatty acid tails can be either...

At cooler temperatures, phospholipids that have 2 saturated fatty acid tails (straight tails) tend to get more rigid / dense because they can more easily pack together. Phospholipids with unsaturated fatty acid tails (bent tails) don't end up getting as rigid / dense, allowing the membrane to stay fluid at lower temperatures. Cholesterol embedded in the phospholipid bilayer also helps it stay more fluid at lower temperatures.

NOTE: Phospholipid bilayers have the consistency of oil-based salad dressing. It may seem weak but it's strong enough to act as a separator between the environment inside and the environment outside. Water from one-side can move to the other but does so very rarely -- a single molecule may sneak through the layer every now and then. Aquaporins are proteins embedded in the phospholipid bilayer that allow water to rapidly pass (when needed).

Examples of molecules that can be embedded in or attached to the phospholipid bilayer include...

NOTE: See first diagram in this section for an example of each of the molecules listed above.

The term facilitated diffusion refers to the movement of molecules across the membrane via proteins embedded in the membrane (e.g. channel proteins and/or carrier proteins). These molecules wouldn't be able to cross the membrane by themselves. For example, the sodium potassium pump (carrier protein) helps sodium and potassium ions move across the cell membrane by opening/closing its gates.

History of Modern Cell Theory

The first record of a cell was in 1665 when Robert Hooke published a book called The Micrographia. The book contains drawings of observations he made while looking at various dead organisms through a rudimentary microscope.

A few years later, a Dutch lenscrafter by the name of Antonie Van Leeuwenhoek decided to use his expertise to craft a better microscope to better observe living cells / organisms. For example, he was able to observe sperm and Protists (unicellular organisms while he dubbed animalcules).

In the 1830s, Matthias Schleiden and Theodore Schwann began laying the groundwork for modern cell theory. They came up with the idea that...

  1. all life is composed of one or more cells.
  2. a cell is the basic unit of life.

They also suspected that cells come from other cells, but didn't know for sure if that was the only way they were produced. It was Robert Remak that in the mid-1800s established that...

  1. all cells come from other cells.

NOTE: The credit for this sometimes goes to Rudolph Virchoi but it's been established that he was a plagiarist.

It's still an open question as to how the first / initial cell came to be. The current working theory is that, 3.5 billion years ago, phospholipids (the molecules that form the membrane of a cell) naturally form bilayers and connect in a circle. A membrane may have naturally encapsulated a set of arbitrary self-replication molecules (e.g. protein or RNA) and that's how the first cell began growing and splitting off.

NOTE: There are an estimated 37 trillion cells in the human body.

Enzymes

An enzyme is a molecule that takes in a specific set of input molecules and transforms them into a specific set of output molecules. The transformation takes the inputs and either ...

Enzymes facilitate these transformations by lowering the activation energy (EAE_A) required for the chemical reactions to take place. Normally this excess energy would come in the form of heat, but enzymes use different mechanisms such as...

... such that other atoms can get close enough to bond.

NOTE: How does heat provide activation energy? More heat = more molecules moving faster = more things bumping into each other faster. 2 molecules may have atoms that want to bond but neighbouring atoms on those molecules may be repelling away with stronger force. Increased speed means the repelling is less effective.

An enzyme is almost always a protein molecule but can also be a RNA-like molecule called a ribozyme.

The general terminology for enzymes are as follows:

Enzymes have a limited set of substrate types that they accept. A substrate will bind to the active site of the enzyme only if it fits into the active site. For example, the following diagram shows 2 substrates binding to an enzyme, the enzyme facilitating their their assembly, then releasing back out.

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

It was previously thought that enzymes had a “lock-and-key” model, similar to how puzzle pieces fit together. Later on it was found out that an enzymes actually induce fit by changing shape slightly when they bind with substrates, such that they can better hold on to those substrates.

Examples of enzymes and what they do:

RNA Polymerase II

Metabolic Pathway

A metabolic pathway is a network/graph of enzymes that produces a final resulting molecule. Each enzyme produces molecules that feed into other enzymes in the pathway, eventually forming the final molecule. The term intermediate refers to an output of one enzyme that’s used as an input by another.

For example, the following graph is the metabolic pathway for gamma-hydroxybutyric acid...

By Anypodetos - Own work, vectorised version of File:GHB metab path.png by User:Meodipt, Public Domain, https://commons.wikimedia.org/w/index.php?curid=8988213

Anabolism

Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).

The process that builds up a molecule from smaller molecules is called anabolism. An enzyme takes in the molecules and creates bonds between them via an endergonic reactions: energy is stored as bonds between the smaller molecules thereby forming the larger molecule.

NOTE: A good way to remember the reaction types... In ENDergonic reactions, the energy ENDs up in a bond. In EXergonic reactions, the energy EXplodes out thereby breaking the bond.

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

An example of anabolism is photosynthesis: plants will bond carbon dioxide gas (CO2CO_2) with water (H2OH_2O) using energy from the sun, creating sugar (C6H12O6C_6H_{12}O_6)

6CO2+6H2O+energyC6H12O6+6O26CO_2 + 6H_2O + energy \to C_6H_{12}O_6 + 6O_2

Catabolism

Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).

The process that breaks down a large molecule into smaller molecules is called catabolism. An enzyme takes in a larger molecule breaks up some of its bonds via exergonic reactions: energy used as bonds in the molecule are release thereby breaking it up into smaller molecules.

NOTE: A good way to remember the reaction types... In ENDergonic reactions, the energy ENDs up in a bond. In EXergonic reactions, the energy EXplodes out thereby breaking the bond.

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

An example of catabolism is cellular respiration: cells will break down the bonds in glucose (C6H12O6+6O2C_6H_{12}O_6 + 6O_2) to release energy, splitting into carbon dioxide (CO2CO_2) and water (H2OH_2O)

C6H12O6+6O26CO2+6H2O+energyC_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O + energy

Nucleotides

Nucleic Acid is a molecule (heteropolymer) that's built up from other molecules called nucleotides (monomers). Nucleic acid comes in 2 flavours: DNA and RNA. Each nucleotide consists of a sugar molecule (ribose in RNA / deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base.

NOTE: It's called nucleic acid because it has some acidic properties to it and DNA is found in the nucleus of a eukaryotic cell. But DNA also in prokaryotic cells and some organelles -- those don't have a nucleus.

By OpenStax - https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Preface, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=30131206

There are 5 base.:

NOTE: T only appears in DNA. In RNA, T is replaced by U.
NOTE: The base is what distinguishes the types of nucleotides from each other. The term nucleotide and base are often used interchangeably.

Two nucleotides connected together are called a base pair. The rules to base pairs are:

DNA

Deoxyribonucleic acid (DNA) is a nucleic acid molecule that contains the instructions needed for the growth/functioning/maintenance of an organism. Depending on the type of organism, DNA is located in different parts fo the cell.

By Zephyris - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=15027555

DNA is composed of two strands of nucleotides that connect at various points in between. The order these nucleotides appear in defines the genetic information/instructions of the organism. For example, a string/sequence of DNA bases: ATATTTTCGATATCCACCA.

DNA strands can be made up of 4 different nucleotide types (bases):

The two nucleotides that make up a connection are called a base pair. In DNA, the rules to base pairs are...

Terminology specific to DNA:

RNA

Ribonucleic acid (RNA) is a nucleic acid molecule used in various ways to facilitate building proteins. It can also act as an enzyme (ribozyme) or contain the genetic information for some viruses.

RNA is commonly composed of a single strand that folds over onto itself.

By Vossman - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=7115139

RNA strands can be made up of 4 different nucleotide types (bases):

The two nucleotides that make up a connection are called a base pair. In RNA, the rules to base pairs are...

NOTE: The rules are similar to DNA, except T is replaced by U. DNA can't have U and RNA can't have T.

Unlike DNA, RNA is transient (lasts for minutes) and comes in multiple flavours:

Chromosome

The genome of eukaryotes are split into linear strands of DNA. These linear DNA strands come in 3 forms...

  1. Chromatin is the normal state, where the DNA is loosely floating around with structural proteins called histones.
  2. Chromatid is the packed form of chromatin, where the DNA is packed using even more structural proteins called scaffold proteins while being replicated. The original chromatid instance and the new chromatid instance are attached together, and they're referred to as sister chromatids.
  3. Chromosome is essentially the same thing as sister chromatids: the original chromatid instance and the new chromatid instance attached together.

By Original uploader was Richard Wheeler at en.wikipedia - Transferred from en.wikipedia to Commons by sevela.p., CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=4017531

NOTE: The terms chromatin, chromatid, and chromosome are often used in ambiguous ways. Depending on the context, the term chromosome may actually be referring to either a chromatin/chromatid, a pair of replicated chromatids that are attached together (sister chromatids), or a pair of replicated chromatids that are attached together (sister chromatids) while they're in their X shape.

At a high-level, the process of DNA replication can be boiled down to 3 steps...

  1. The chromatin is copied. Each instance is now referred to as a chromatid and is attached to the other (sister chromatid) via proteins called cohesins.
  2. The sister chromatids condense and start to separate in an X shape. The section they remain connected at is a segment of DNA called the centromere.
  3. The sister chromatids are pulled apart. Each instance is now reverted back to being referred to as chromatin.
NOTE: Don't confuse DNA replication (above) for organism reproduction (below). Replication (above) is taking about how the DNA is being cloned. Reproduction (below) is talking about how species makes offspring.

Most eukaryotic species are diploid, meaning that their linear DNA strands come in matching pairs where each pair contains different versions of the same set of genes (homologous pairs). When these organisms reproduce, they generate special cells known as haploid cells that only contain 1 strand from each pair. Two haploid cells mix their DNA to create a final diploid offspring (e.g. a sperm cell and an ova cell).

By National Human Genome Research Institute, http://www.genome.gov/Images/EdKit/bio1c_large.gif, Public Domain, https://commons.wikimedia.org/w/index.php?curid=2132905

NOTE: This isn't entirely true? Some eukaryote species can replicate by cloning themselves (some reptiles?). Their eggs don't need sperm.

Certain diploid eukaryotic species (some mammals/snakes/insects/etc..) have an extra pair that aren't alternate versions of each other but instead are totally different and used to determine the sex of the offspring. This extra pair are called sex chromosomes / XY chromosomes, and it determines the sex of the organism. The X and the Y refer to the chromosome types that can appear in the pair -- XX results in a female, while XY results in a male.

The non-sex chromosome pairs are referred to as autosomes.

By National Human Genome Research Institute, http://www.genome.gov/Images/EdKit/bio1c_large.gif, Public Domain, https://commons.wikimedia.org/w/index.php?curid=2132905

NOTE: An example straight from the material: As a real example, let's consider a gene on chromosome 9 that determines blood type (A, B, AB, or O). It's possible for a person to have two identical copies of this gene, one on each homologous chromosome—for example, you may have a double dose of the gene version for type A. On the other hand, you may have two different gene versions on your two homologous chromosomes, such as one for type A and one for type B (giving AB blood).

Reproduction

Reproduction is when an organism generates offspring. It comes in 2 forms: asexual and sexual.

Asexual reproduction is when offspring is created using the genetic material from 1 parent. The offspring are essentially copies of the parent in terms of their genetic material (clone). Examples of asexual reproduction include:

Sexual reproduction is when offspring is created by fusing genetic material from 2 parents. The offspring has a mixture of genetic material from both parents. An example of sexual reproduction is when a gamete cells merge to create the offspring. Gamete cells have half the genetic information from the original parent, and when they merge they mix that genetic material to create the new genetic material for the offspring. Male gamete cells are called sperm, while female gamete cells are called ova or eggs.

NOTE: In some cases, the genetic material being fused in sexual reproduction may be from the same parent. Answer to a question on the site... it is still sexual, because sexual reproduction means fusion of male and female gametes, doesn't matter if they're from the same plant. polliation is the transfer of pollengrains from anther to stigma, further to reach ovary. in case of a bisexual flower, it is called self-pollination.when two different flowers pollinate it is cross pollination.

Adenosine Triphosphate

Adenosine Triphosphate (ATP) is a molecule that provides energy to drive various biological processes (e.g. muscle contractions). The third phosphoral group at the very end has a high-energy bond. When broken, energy is released and the resulting molecules are the broken up phosphoral group and Adenosine Diphosphate (ADP).

NOTE: High-energy bonds are actually a thing: A chemical bond whose hydrolysis results in the generation of 30kJ (7kcal) of energy or, if coupled to an energetically unfavourable reaction, can drive that reaction forward. (https://www.genscript.com/molecular-biology-glossary/1364/high-energy-bond)

By Muessig - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=27614630

ATP is produced in the mitochondria. Similar to how the mitochondria is referred to as the powerhouse of the cell, ATP is often referred to as the energy currency of the cell / energy store for the cell.

Transport

There are 2 different types of mechanism used to transport molecules in and out of a cell: passive transport and active transport.

Passive transport is when molecules naturally move towards the gradient. In this context, gradient refers to the natural direction in which things are supposed to go -- no explicit energy is needed to move/push it along, it just moves in that direction by virtue of some implicit property.

Active transport is when molecules use energy (e.g. ATP) to move against their gradient. It's the opposite of passive transport -- energy is explicitly used to drive a molecule to where it naturally / normally wouldn't go. An example of active transport is the "sodium potassium pump" enzyme: ATP is used to force open/close the ends of the enzyme, which allow sodium and potassium to be exchanged across the cell membrane.

Note that the active transport in the example above is the opening/closing of the enzyme ends, not the exchange of sodium and potassium. Energy (ATP) is being used to shape-shift the enzyme to open/close (active transport) while the sodium and potassium are passively entering and exiting the gates (passive transport via facilitated diffusion).

Osmosis

Osmosis is the passive transport of solvent molecules (typically water), across a semipermeable membrane, from areas where solutes are less concentrated to areas where solutes are more concentrated.

For example, imagine you have a semipermeabl membrane that allows water molecules (solvent) to pass but not sodium (solute). That membrane is separating 2 regions, where the ...

There will be a net movement of some water molecules from the left region (lower solute concentration) to the right region (higher solute concentration).

By OpenStax - https://cnx.org/contents/FPtK1zmh@8.25:fEI3C8Ot@10/Preface, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=30131189

NOTE: Another diagram that may make more sense conceptually: https://commons.wikimedia.org/wiki/File:Osmosis_diagram.svg

There are 2 reasons why osmosis happens. The first is that the semipermeable membrane will only allow certain types of molecules to pass through. If the semipermeable membrane is gated by ...

The higher the concentration of solute molecules, the less likely it is for the solvent molecules to reach a pore in the semipermeable membrane. The side with the lower concentration of solute molecules is more likely to have a solvent molecule reach a pore than the other way around.

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

The second reason is that, depending on the charge of solvent and charge of solute, the solvent may be attracted to the solute. More solute = more chance that a solvent gets attracted to it instead of crossing a pore in the membrane. For example, if the solvent is water and the solute is sodium, the weakly negative charge of the oxygen atom in a water molecule may get attracted to the positive charge of the sodium ion.

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

Tonicity is the amount of pressure applied to a semipermeable membrane due to osmosis. In other words, it's the amount of water that flows in or out of a cell due to the type of solution it's put in. A ...

This work by Kasra Faghihi is licensed under a Creative Commons Attribution 4.0 International License.

NOTE: The prefix is referring to the amount of solute in the solution relative to the cell. Hyper = more. Hypo = less. Iso = same.

The following is a micrograph of the red blood cells in solutions of different tonicity. Notice how they shrivel in a hypertonic solution (lose water) and expand in a hypotonic solution (gain water).

By Zephyris - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=18401754

Photosynthesis

Photosynthesis is the process by which certain organisms convert light energy (photons) to chemical energy (sugars). These organisms are called Photoautotrophs, and they include ...

NOTE: Another way to think of photosynthesis is that it uses light energy (PHOTOsynthesis) to synthesize (photoSYNTHESIS) sugars.
NOTE: Chloroplast and cyanobacterium share a similar structure. It's speculated that they have the same parent organism: that parent formed an endosymbiotic relationship with a larger cell and eventually became the chloroplast organelle.

The overall chemical reaction for this is 6CO2+6H2O+energyC6H12O6+6O26CO_2 + 6H_2O + energy \to C_6H_{12}O_6 + 6O_2. Carbon dioxide gas (CO2CO_2) bonds with water (H2OH_2O) using energy from the sun (photons), creating glucose (C6H12O6C_6H_{12}O_6).

This reaction happens in 2 steps:

  1. Light-dependent reactions: Energy molecules are created from water and photos, with oxygen being a byproduct.

    This occurs in a thylakoid membrane.

    Ultrastructure of a chloroplast.

  2. Calvin cycle: It's a cyclical process that requires multiple iterations (3?) to produce a single glucose molecule. Each cycle, ATP and NADPH are used for energy (producing ADP and NADP+ respectively), while the carbon dioxide (CO2CO_2) is used as a source of carbons for the resulting glucose.

    This occurs in the stroma.

    Ultrastructure of a chloroplast.

The following workflow diagram provides a ultra-simple high-level overview of the processes that take place. Note that this doesn't specify how many of each molecule get input / output, nor does it provide a complete set of a input / output molecules for each reaction.

Graphviz Dot Diagram

Cellular Respiration

Cellular respiration is the process by which certain organisms convert glucose (sugar) to energy. These organisms include ...

NOTE: Remember that all eukaryotes have mitochondria -- both plant and animal cells. Unsure if all bacteria can perform cellular respiration?

The overall chemical reaction for this is C6H12O6+6O26CO2+6H2O+energyC_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O + energy. Glucose (C6H12O6C_6H_{12}O_6) and oxygen (O2O_2) break down into carbon dioxide gas (CO2CO_2), water (H2OH_2O), and energy (roughly 38 ATP molecules and some heat).

NOTE: The number of ATPs actually generated is variable and dependent on many factors, but 38 is the generally agreed upon number.

The reaction happens in 3 steps:

  1. Glycolysis: The carbon backbone of the glucose molecule is split, creating 2 Pyruvate molecules along with water and several other molecules. This is an anaerobic process (no oxygen needed) that nets 2 ATP. This happens in the cytoplasm of cells.

    Eukaryote with cell ribosomes highlighted

  2. Krebs cycle: The pyruvate molecules get further sliced and diced with other molecules. This is an aerobic process (requires oxygen) that nets 2 ATP. This happens in the matrix of the mitochondria.

    Mitochondria

  3. Oxidative phosphorylation: Produces around 34 ATP. This is an aerobic process (requires oxygen) that nets roughly 34 ATP (bulk of conversions). This happens in the electron transport chain section of the mitochondria (inner membrane).

    Mitochondria

NOTE: The material says that, technically step 3 doesn't have to happen after step 2 but it usually does.

Because the Krebs cycle and the oxidative phosphorylation are aerobic processes (require oxygen), if no oxygen is present the output of glycolysis goes through a process called fermentation. Fermentation is an anaerobic process (no oxygen required). Depending on the organism, it'll end up producing either...

Fermentation does produce ATP, but much less so than Kerbs cycle + oxidative phosphorylation.

For example, if a human is vigorously running, that human may not have enough oxygen available to trigger the Krebs cycle / oxidative phosphorylation (steps 2 and 3). As such, the output from glycolysis (step 1) will end up going through lactic acid fermentation instead.

The following workflow diagram provides a ultra-simple high-level overview of the processes that take place. Note that this doesn't specify how many of each molecule get input / output, nor does it provide a complete set of a input / output molecules for each reaction.

Graphviz Dot Diagram

Sodium Potassium Pump

The sodium potassium pump is an transmembrane enzyme that allows the exchange of sodium ions and potassium ions across the cell membrane by opening and closing its ends.

By LadyofHats Mariana Ruiz Villarreal - Own work. Image renamed from Image:Sodium-Potassium_pump.svg, Public Domain, https://commons.wikimedia.org/w/index.php?curid=3981038

Only 1 end of the enzyme is open at a time. When the...

Since both potassium and sodium have a positive charge and an an unequal number are being exchanged each cycle (3 sodium out vs 2 potassium in), the intracellular space will be more positive than the extracellular space.

This charge difference is further reinforced by membrane channel proteins which allow potassium ions to flow across the membrane (potassium channels). Since there's a higher concentration of potassium ions inside the cell, those potassium ions have a higher chance of flowing through the channel to the outside. Some percentage may be impeded by the slightly more positive charge on the outside, but overall more will make it to the outside than stay on the inside.

This charge difference is referred to as the resting membrane potential for a cell.

Microscopy

Microscopes are devices used to magnify (zoom in) on objects, such that you can see things that you normally would be too small to see on your own. The term microscope comes from the words...

A picture taken through a microscope is called a micrograph. The distinguishing factors for most microscopes or the amount of magnification and the resolution of the output image.

There are different types of microscopes:

Other Terminology

Terminology that's relevant but doesn't fit in any other section goes here.

Density - The mass per unit volume of a substance.

Specific heat capacity - The amount of heat needed to raise the temperature of one gram of a substance by one degree Celsius.

Heat of vaporization - The amount of energy needed to change one gram of a liquid substance to a gas at constant temperature.

Endosymbiosis - A form of symbiosis where one organism lives inside of of the other (e.g. gut bacteria lives in our colon). The prefix endo means within.

Diffusion - A physical process where molecules of a material move from an area of high concentration (where there are many molecules) to an area of low concentration (where there are fewer molecules) until it has reached equilibrium (molecules evenly spread). See more.

Equilibrium - A state in which opposing forces / influences are balanced. In the context of a concentration gradient, it means the state at which a substance is equally distributed throughout the volume that it's in (roughly).

Permeability - The state or quality of a material or membrane that causes it to allow liquids/gases to pass through it.

Semipermeable - The state or quality of a material or membrane that causes it to allow certain types of molecules to pass through it.

Intracellular - The fluid inside of the cell, which is technically on the inside of the cell membrane (cytoplasm).

Extracellular - The fluid outside of the cell.

NOTE: Technically unsure at which layer the extracellular region begins. Is it outside of the cell membrane? cell wall? cell capsule? I'm pretty sure any fluid outside of the cell membrane qualifies as extracellular, while any fluid inside of the cell membrane qualifies as intracellular (cytoplasm).

Aerobic - A biological process that requires oxygen.

Anaerobic - A biological process that doesn't require oxygen.

Fission - The act of dividing or splitting something into two or more parts.

Homologous - Having the same relation, relative position, or structure. Particularly in biology, it s the existence of a shared ancestry between a pair of structures or genes.

Karyotype - Micrograph image of diploid set of chromosomes, grouped in pairs.